Need more specifics, but are you making sure that the lights are centered on the object and I believe lightsize has a factor in it as well. What are you using to convert. I found that PCS can be quite usefull. As long as all the turret objects are subojects (glued with light, you can use PCS to make them turrets via name change, FP placement and a corresponding TBL assignment (mucho importante).
So far, I've made 3 of my Trek conversions bomber classes. All converted with PCS. I get less headaches with tedious Truespace gluing.
Please give more specifics in programs used and hierarchy structure in Truespace.